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Symbiont communities shape coral physiology and nutrition

DOI

CB Wall, M Kaluhiokalani, BN Popp, MJ Donahue, RD Gates. (2019). Divergent symbiont communities determine the physiology and nutrition of a reef coral across a light-availability gradient. The ISME Journal.

Reef corals are mixotrophic organisms relying on symbiont-derived photoautotrophy and water column heterotrophy. Coral endosymbionts (Family: Symbiodiniaceae), while typically considered mutualists, display a range of species-specific and environmentally mediated opportunism in their interactions with coral hosts, potentially requiring corals to rely more on heterotrophy to avoid declines in performance. To test the influence of symbiont communities on coral physiology (tissue biomass, symbiont density, photopigmentation) and nutrition (δ13C, δ15N), we sampled Montipora capitata colonies dominated by a specialist symbiont Cladocopium spp. or a putative opportunist Durusdinium glynnii (hereafter, C- or D-colonies) from Kāne‘ohe Bay, Hawai‘i, across gradients in photosynthetically active radiation (PAR) (1 - 10 m depth) during summer and winter.

Directory information

PanKBay-isotopes_pub.html

html file for Rmd output

PanKBay-isotopes_pub.Rmd

R markdown for project

PanKBay isotopes.Rproj

R project to run Rmd and directory

DATA houses the following folders and files

coast_n83.shp : shape files for making site maps
environmental :

  • folder sea level for sea-level correction
    columns
    stationID = Moku o Lo'e weather station
    datum = mean sea level (MSL)
    TimeUTC = time in UTC
    TideHT = tidal height in meters
    (other columns NA)

  • folder temp and light for raw data collected on the reef

  • PanKBay_nutrients.csv for dissolved inorganic nutrients
    columns
    Date = date of collection
    Reef = reef IDs, F=fringe, R=patch reef
    Location = northwest NW, northeast NE, central west CW, southeast SE, southwest SW
    phosphate, silicate, N+N (nitrate+nitrite), ammonium = all in μmol L-1

  • Reefs_lat_long.csv for mapping sampling sites
    columns
    Site = Reef ID as cardinal directions and Reef number
    latitude and longitude = in decimal degrees

qPCR

  • eds files (for StepOne Platform) and associated .txt files with qPCR plate reads

  • isotopes_SW_all times.csv
    seawater and plankton isotopes collected at the sample sites in each season
    columns
    Season = summer or winter (northern hemisphere)
    Sampling.date = date as "yyyymmdd"
    Reef = F for fringe reef, R for patch reef, and reef number
    Location = NW, SE, NE, SW for north (N) south (S) and east (E) or west (W)
    Region = northern or southern Kāne'ohe Bay
    Habitat.type = fringe or patch reef
    North.South.ID = arbitrary ID #
    SW.fraction..um = the size fraction of seawater in μm
    ug.N = ug of nitrogen
    d15N = δ15N in permil
    ug.C = ug of carbon
    d13C = δ13C in permil

  • mastersheet_PanKBAY.csv
    all response variables from physiology and isotope analyses (prior to calculation of C-D dominance)
    columns
    Date = date of collection as mm/dd/yy
    Season = summer or winter (northern hemisphere)
    Reef = F for fringe reef, R for patch reef, and reef number
    Location = NW, SE, NE, SW for north (N) south (S) and east (E) or west (W)
    Reef.type = fringe or patch reef Bay.region = northern or southern Kāne'ohe Bay
    Time.of.collection = time for tidal correction
    Depth..m = colony depth in meters
    Sample.ID = arbitrary sample ID
    total.blastate.ml = total tissue extract (blastate) in ml
    surface.area.cm2 = colony surface area in cm2
    cells.ml = symbiont densities in cells per ml blastate
    ug.chl.a.ml = μg of chlorophyll a per ml blastate
    ug.chl.c2.ml = μg of chlorophyll a per ml blastate
    mg.biomass.ml = mg of host biomass per ml blastate
    host..mass.mg = lyophilized host biomass for isotope analysis
    host..ug.N = μg of nitrogen in host tissue
    host..d15N = δ15N of host tissues in permil
    host..ug.C = μg of carbon in host tissue
    host..d13C = δ13C of host tissues in permil
    host..C.N = molar ratio of carbon : nitrogen in symbiont tissues
    symb..mass.mg = lyophilized symbiont biomass for isotope analysis
    symb..ug.N = μg of nitrogen in symbiont tissue
    symb..d15N = δ15N of symbiont tissues in permil
    symb..ug.C = μg of carbon in host tissue
    symb..d13C = δ13C of symbiont tissues in permil
    symb..C.N = molar ratio of carbon : nitrogen in symbiont tissues
    d15N..host.symb = difference in δ15N of host minus symbiont in permil
    d13C..host.symb = difference in δ13C of host minus symbiont in permil
    d13C..skel = δ13C of coral skeletal carbonates in permil
    d18O.skel = δ18O of coral skeletal carbonates in permil

  • PanKBay_summer_qPCR.csv
    compiled qPCR data for summer samples (post pipeline [detailed in Rmd file])

  • PanKBay_winter_qPCR
    compiled qPCR data for winter samples (post pipeline [detailed in Rmd file])
    columns
    Colony = arbitrary ID
    Date = mm/dd/yy
    Depth..m = coral depth in meters
    Latitude and Longitude = in decimal degrees
    Time = hh:mm
    Season = summer and winter (northern hemisphere)
    Reef.type = fringe or patch reef
    Bay.region = northern or southern Kāne'ohe Bay
    Reef = reef ID
    Location = NE, NW, SE, SW
    Sample.ID = arbitrary ID for colony at each reef location
    File.Name = the qPCR file where data originated
    C.CT.mean = mean CT value for 2 reps for Cladocopium
    D.CT.mean = mean CT value for 2 reps for Durusdinium
    C.CT.sd = standard deviation CT value for 2 reps for Cladocopium
    D.CT.sd = standard deviation CT value for 2 reps for Durusdinium
    propC = proportion of community as percentage Cladocopium
    propD = proportion of community as percentage Durusdinium
    Dom = dominant symbiont at > 50%
    Mix = mixture of symbionts as all C, all D, D>C or C>D

FIGURES houses exported figures

environmental :

  • folder: unused are figures used in analysis but not published

  • pdfs for daily light integral (DLI) and photosynthetically active radiation (PAR) at the 2m depth only (for comparison)

  • pdf for coefficent plots for DLI and PAR fitting

  • all.nutrients.pdf (DIN)

  • DLI.bar.pdf (mean +/-SE bar plot)

  • DLIcalc.alldepths.pdf (DLI at 3 depth zones)

  • iso.sources.KBay.pdf (mean +/- SE, isotope sources, end members)

  • KBaymap.pdf (map and sites)

  • Temp.allsites.pdf (temperature at 2m for each site)

isotopes :

  • isotope_multipanel.pdf (carbon isotope figures)
  • suppm.CNboxplot.pdf (boxplots for C:N data, host and symbionts)
  • suppm.Cskel.pdf (skeletal carbon and oxygen isotope figures)
  • suppm.nitrogen.pdf (nitrogen isotope figures)

models :

  • variance.pdf (model random effect [location] proportion of variance)

multivariate :

  • PCx4.pdf (PCA with 4 plots of differing categories)

physiology :

  • physio_multipanel.pdf (multipanel of all physiology metrics)

regressions :

  • symb.isotope_by.symb.phys.pdf (regression of symbiont physiology vs. symbiont carbon isotope values)
  • symb.by_HS.d13C.pdf (regression of symbiont physiology vs. carbon host-symbiont isotopes values)

symbionts :

  • Light by Depth_symbs.pdf (calculations for DLI at the coral surface)
  • Symb_Season_Light_logistic.pdf (logistic regression histograms of symbiont distributions)
  • Symbionts_by_Season_depth.pdf (probability of Durusdinium across depth)

M capitata_KBay_Wall.png (coral figure)

OUTPUT houses exported outputs and compiled data

  • C_D sample size.csv (sample size for C- and D-dominated corals)
  • data.all.csv (all physiology, isotope, and symbiont community data)
  • kd.all.csv (light attenuation coefficients for each site)
  • Light attenuation_table.csv (light DLI mean +/-SE at <1m and attenuation relative to this at 2m and 8m-depth)
  • light coeffs_factor.csv (coefficients of models for ligh-at-depth calculations)
  • season.DLI.csv (DLI mean +/- SE at each site, in each season)

About

This project examines the isotope composition of reef corals across seasons, sites, and depth.

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